The question is why not treat handguns like machine guns? The process to purchase a machine gun (according to the NFA and related amendments) Let's assume that the NFA works in preventing crimes committed with machine guns. Why would any law-abiding gun owner protest the registration of handguns?
One of my biggest objections to gun registration and licensing of any kind is that it opens up the doors for discrimination.
Registration usually requires chief law enforcement officer permission meaning county sheriffs and police chiefs would essentially have the final say over whether one had the right to own a handgun or not. Gun registration can be used as a tool by biased law enforcement officers to dissuade would-be gun owners. Especially those who are racial, sexual, or religious minorities.